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Crystal structure of PenI beta-lactamase from Burkholderia pseudomallei at pH9.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P74 PDB ENTRY 2p74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 298 25% PEG8000, 0.1M CHESS, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.94 36.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.395 α = 90 b = 52.771 β = 92.55 c = 50.471 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2010-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.18 50 96.4 0.088 14.8 4.04 68591
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 2p74 1.18 15 66491 66491 2064 94.2 0.115 0.115 0.1138 0.1223 0.1528 0.158 RANDOM 10.68
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 28 1939 2320.23
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.089 s_non_zero_chiral_vol 0.088 s_zero_chiral_vol 0.08 s_anti_bump_dis_restr 0.041 s_from_restr_planes 0.0378 s_angle_d 0.031 s_similar_adp_cmpnt 0.021 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1987 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 19
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing